VISTA: visualizing the spatial transcriptome of the C.elegans nervous system

Area of Science:

• Neuroscience
• Genomics
• Computational Biology

Background:

• Spatial transcriptomics aims to map gene expression within tissues at single-cell resolution.
• Existing technologies face limitations in balancing resolution and whole-transcriptome coverage.
• The nematode worm Caenorhabditis elegans offers a unique model for high-resolution spatial transcriptomics due to its invariant lineage and available datasets.

Purpose of the Study:

• To present VISTA, a novel tool for visualizing the spatial transcriptome of C. elegans, with a focus on the nervous system.
• To enable researchers to explore gene expression patterns at the single-neuron level.
• To facilitate the identification of novel gene expression patterns and resolve cellular identities.

Main Methods:

• Leveraging existing single-cell transcriptome and spatial datasets for C. elegans.
• Developing a visualization platform (VISTA) that displays gene expression as a "spatial heatmap" across neurons.
• Allowing users to query specific genes and view their expression levels (Transcripts Per Million) in individual cells.

Main Results:

• VISTA successfully visualizes the spatial transcriptome of C. elegans neurons.
• The tool facilitates the identification of novel gene expression patterns in specific neurons.
• VISTA aids in resolving cellular identities for ambiguous expression patterns from in vivo reporter genes.

Conclusions:

• VISTA provides an accessible method for obtaining gene-level snapshots of the neuronal spatial transcriptome in C. elegans.
• The tool is expected to advance studies on neuron-specific gene expression and regulation.
• VISTA serves as a template for future high-resolution spatial transcriptome visualizations in other species.